A power hungry alien, Javkor, is out to become the largest illicit alien arms dealer in New York. MiB is closing in on him, but Javkor has a secret weapon, a sexy alien named Veronica. She seduces Frank The Pug, so that he will get Javkor's gang into MiB's secured vault where the most powerful weapons in the galaxy are kept. Frank falls hard for Veronica as she plays him like a bow fiddle. In the meantime, the MiB appear to be one step behind the scam, unaware that Frank is selling them out ... or are they? Frank eventually sneaks the bad guys into the MiB vault, but Kay and Jay are inside waiting, having figured out Javkor's scheme early on. Javkor, Veronica and the rest of the alien gang are captured, foiling their plans. Faced with the truth about Veronica, Frank is heartbroken but comforted by Kay and Jay who take him out for a steak to cheer him up.

Alien "cops" from the planet Kalafatic and have come to Earth to round up that last of the "violators" anyone who has committed crimes against their planet. As they arrive through MiB Customs, the first on their list are the Twins. The Kalafatic points his weapon and the twins disappear. Jay and Kay are on the scene but as they are about to apprehend the Kalafatics, one of them grabs a worm guy as hostage and turns his weapon on himself thus disappearing with the worm guy in tow. Kay explains the twins and the worm guy haven't been destroyed but "teleported" by the Kalafatic device. Kay teleports Jay with the confiscated teleporter, betting that it will land Jay at the same location with the escaped Kalfatic and the worm guy. At the very same time the Kalafatic has decided to release the worm guy and teleports him back to MiB. In the vortex created by the teleportation Jay and the worm guy's molecules merge and become mixed. Jay slowly begins to take on the worm's personality and has a caffeine habit that just won't quit. Kay is left with a pint-sized worm-guy partner who is now more like Jay than Jay. They head out to capture the renegade Kalafatic before he can get to Jeebs, the "last violator" and rescue the twins from their Kalafatic prison cell.

When an escape pod from a Russian space station jettisons away and eventually crash lands in the Antarctic, Kay and Jay head south, way south, to investigate. Unbeknownst to them, the worm guys have stowed away, thinking they are headed to South America, home of the coffee bean. What Kay and Jay discover is that Alpha was in the pod, his body having merged with Dack, Jeebs' obnoxious brother, while Apha and Dack were floating in space. With the help of Jeebs who arrives in his pod, Dack and Alpha unearth a "Bioship" long buried beneath the Antarctic ice. If Alpha/Dack can commandeer the ship, they can hold the world hostage with the ship's power. But with the inadvertent help of the Worm Guys, Kay and Jay bring down the ship, separate Dack from Alpha and bury Alpha in an avalanche.

A series of high-tech thefts lead Kay and Jay to the Darkons, a race of hostile Shadow Creatures with an aversion to sunlight, but a penchant for Earth as a future colony. During the investigation, Kay is hit with a Dark Ray by the alien leader, Nakar, and blinded. While Elle works to restore Kay's sight, Kay and Jay (along with the stowaway Worm Guys) must travel to the moon to thwart the Darkons from assembling a Graviton array, thus locking the planetoid into a permanent eclipse of Earth.

When a rampaging alien called a Metaphite breaks out of its cocoon and threatens Phoenix, MiB is called in to stop it. Unfortunately, all efforts prove useless against the giant alien that is basically a living nuclear reactor. The only solution is to use a "Time Jumper' to travel back one hundred and thirty years in the past when the Metaphite cocoon is vulnerable. Upon arriving smack dab in the middle of the wild west, Kay and Jay locate the cocoon only to be ambushed by another alien, a Vexron, which grabs the Metaphite cocoon and escapes. Kay and Jay (soon joined by Elle) must race to save the future by figuring out who of western town folks is actually the Vexron in a human suit. Along the way there's an old-fashioned "high noon" gunfight, a barroom brawl and a prison break out. In a climatic chase, our agents thwart the Vexron and capture the Metaphite, just in the nick of time to save the future.

A Bug Queen is in town with her two bug escorts and it is up to MiB to find her before she can lay her eggs and infest the city. To make matters more complicated, the Emperor Worm is also in town, mutilating his English and basically making life tough on the Worm Guys. The Emperor Worm insists on being put up in a hotel worthy of his stature which, unfortunately, turns out to be the same one which the Bug Queen has chosen for her lair. The Emperor is taken hostage and it's up to Kay, Jay, and Elle (along with some unsolicited help from the Worms Guys who are trying to score brownie points with the Emperor) to rescue him and neutralize the Bug threat before it gets out of hand.

Jay and Kay are summoned to a remote MIB submarine outpost manned by the cabin-fevered Agent C, in order to stop intergalactic terrorist/zealot Quin'toon, who has taken alien hostages and plans to raise the ancient, long-abandoned, alien-built continent of Atlantis from the ocean floor. As Zed points out, this would not only blow MIB's "cover-up of aliens' existence", but worse, cause tidal waves of such force as to wipe out half the East Coast. During the mission, Jay is inoculated with an amphibious serum to allow him to survive the perilous depths, but is revolted to discover that its also given him gills and webbed fingers. Jay and Kay manage to overcome Quin'toon and his Robot minions and stop the Atlantis raising machinery at the last moment. But not fast enough: a killer wave is heading for a populated tropical island and our MiB duo are the only ones who can stop it.

Zed makes a stunning announcement: He's retiring; he's decided he's too old and weary to lead MiB into the next century. Kay will be his replacement; Jay will get a new partner. Zed is given a retirement party, neuralized and immediately "re-located" to pursue a new life fishing on Long Island. But it seems Zed's timing couldn't be worse: Alpha is back, is up to something big and must be stopped. With Kay promoted to chief, Jay is eager to get himself a new junior partner he can boss around. But his bubble is burst when he's assigned a new partner - Elle. Out in the field, Elle and Jay locate Alpha, who sports formidable new body parts and powers. Jay gets captured. Alpha tortures and brain probes Jay, who finally "breaks", revealing to Alpha where Zed has been re-located to. After Alpha takes off in pursuit of Zed, Elle rescues Jay and lets him know the truth: Zed was never really retired or neuralized. It was all a ruse, part of a sting operation to draw Alpha out into the open, where he could be ambushed by MiB agents. Jay was kept in the dark, so that when he was captured by Alpha (which Elle helped orchestrate) the brain probe wouldn't give the plan away. As Jay stews over being used both as a patsy and as bait, they arrive on Long Island to discover that the sting has gone awry: Alpha figured it out, and has gotten the drop on the MiB ambush. In an action-packed climax set on the dune-filled beach, Jay redeems his wounded pride, and Zed proves he's anything but over the hill, when they team up to destroy Alpha ... who in the end reverts to his human form and is put away for good.

Fighting off a cold, Jay inadvertently swallows an alien embryo thinking it's a vitamin. Now he's pregnant, and to compound matters, the real mother, known as a Bobbalot becomes Jay's shadow, following him everywhere to ensure her unborn child's well being. Meanwhile, Jay and Kay are after the Fmecks who are stealing some of New York's most famous landmarks with the aid of a Shrink Ray, which reduces each structure to a fraction of its normal size. While on stake out, Elle gets trapped inside the Statue of Liberty when it is shrunk by the Fmecks. Not good news for Jay, since Elle is the only one who can deliver the baby without it exploding out of Jay's chest. With Jay and the baby Bobbalot's life hanging in the balance, the action culminates at Coney Island, where the MiB get the drop of the pesky Fmecks. Elle is resized and delivers the alien baby just in time to help thwart the Fmecks. In the end, Jay takes on the role of the proud papa.

When the Worm Guys apparently are responsible for a near nuclear meltdown at MiB, Zed orders them deported. But Jay comes across evidence that suggests that the Worm Guys were merely in the wrong place at the wrong time and that the meltdown was an act of sabotage. To prove his theory, Jay must put his MiB career on the line by disobeying orders and replacing the Worm Guys with quick clones before their transport ship blasts off. Together with the Worm Guys, Jay pieces together the mystery and discovers that the real perp is an unassuming MiB janitor named Zelgar who is bent on carrying out his revenge on those he feels have slighted him (including Kay). In the end, Jay and the Worms rescue Kay and the alien hostages, defeat Zelgar, and clear their good names.

Kay AND Jay track an unregistered, unidentified alien arrival, who turns out to be the King of a slug-like race called Tunstons. These robosuited aliens are plotting to take over New York City, and then the world, by covering ft in the bacterial ooze that Tunstons need to survive. Unfortunately, the giant robosuit created for the KING is damaged in a battle with Kay and Jay, so the alien King must take up temporary residence in Frank the Pug. As most everyone in the city gets sick from the bacterial ooze, the Tunston King plots to seed the clouds and trigger a bacterial rain that will accelerate the plan to turn Earth into a Tunston colony. Kay and Jay must stop the Tunstons and find a way to save Frank.

Kay and Jay are called in to investigate when a 5,000-year-old Mummy comes to life, ransacks a museum and escapes. They bring with them an unlikely expert in Egyptology...Frank The Pug. The MiB agents and Frank soon determine that the Mummy is actually an ancient alien scout sent by a war-hungry race called the Hyperians. Just as Kay, Jay and Frank are about to thwart the rampaging Hyperian Mummy, Jeebs whisks the alien back to Egypt in his transport pod. Our trio follows, with Frank withholding the fact he and Jeebs are both actually after the powerful "Scepter of Socclarian" used by the Hyperians. While Kay and Jay engage the alien Mummy in an exciting battle in one of the pyramids, Frank and- Jeebs find the "Stargate"-like passageway leading to Hyperia. They pass through and, upon arriving in Hyperia, Frank is mistaken for a living deity and worshipped by the alien race. Eventually, the Mummy also passes through the gateway and Kay and Jay realize that they must seal off the passageway from both sides in order to stop the Hyperians from invading Earth. In the end, Frank is exposed as a fraud by Jeebs while Kay and Jay use the opportunity to escape the Hyperians. Our heroes are barely able to safely pass back through gateway and blow it up behind them, saving the earth in the process.

The new leader of a terrorist race of aliens called Stellairians wants to embark on a new era of peace and comes to Earth for negotiations ... bringing along his spoiled teenage daughter. The Stellairians age rapidly in Earth's atmosphere - about 100 years in a day - so Kima is reminded to take her hypo-spray, located on a chain around her neck. Kay and Jay are assigned baby-sitting duty, and take Kima to the mall - where a group of Frostifarian Kidnappers (who had their icy planet scorched by Skon) create a diversion and nab Kima. During the chase, her hypo-spray comes loose and accidentally exposes Kay to the anti-aging serum. As a result, he begins to regress at a rapid rate - going from adult Kay, to a 12-year-old, to a three-year-old Toddler, and finally to a Baby. In his infant form, Kay...along with Jay... must find Kima before she becomes too old and dies, and before her father Skon blows up the planet, as he threatens if his daughter is not returned safely.

After Jay takes the LTD for a joyride...Zed pronounces him too much of loose cannon - and decides to terminate Jay as an MIB agent. Jay thinks it's a bluff to scare him...until he sees the neuralizer! Jay is sent back into his old life, where he's welcomed by his old cop buddies. Meanwhile, at MiB, they're getting hints of an impending disaster: The Bugs are back and they're gonna attack. As Jay is getting re-acclimated to his old life, he keeps having nagging memories and Close Encounter-type dreams: images of Bugs. Kay, now a total stranger to Jay, pays him a visit and realizes the neuralization wasn't complete: Jay may have information about the bugs. Kay reveals to Jay that he has spent the last three years as a member of the covert MIB. Jay doesn't believe a word of it. But when they arrive at MIB everybody knows Jay...he doesn't know what to think. None of Elle's techniques for memory recovery work on Jay. Its not until Kay calls Jay by his nickname "Slick" that Jay's complete memory of MiB is restored. Jay is back in Black and ready for action...if he wants.